Habitat Suitability for Upper Salmon Subbasin Multiple Reach Assessments

¹ Biomark, Inc.

1 Introduction

The Bureau of Reclamation (BOR), Idaho Governor’s Office of Species Conservation (OSC), and an interdisciplinary team of partners have assembled an Upper Salmon Assessment Team to complete biologic and geomorphic analyses in support of future project identification, prioritization, and design in the Upper Salmon Subbasin, Idaho. The biologic and geomorphic analyses are being lead by Biomark Inc. (Biomark) and Rio Applied Science and Engineering (Rio ASE), respectively. Past efforts from the team resulted in the development of a watershed-scale Integrated Rehabilitation Assessment (IRA) in the Lemhi, Pahsimeroi, and Upper Salmon (Sawtooth Valley) watersheds. This initial phase of the project identified the “problem” by spatially quantifying capacity limitations for spring/summer Chinook salmon and summer run steelhead within a geomorphic context across these three watersheds. The second phase, termed the Multiple Reach Assessments (MRA), includes identifying appropriate and focused “solutions” to the identified capacity problems within four valley segments: Upper Lemhi, Lower Lemhi, Lower Pahsimeroi, and Upper Salmon (Decker Flats). To achieve this goal, the team will collaboratively summarize existing and targeted physical habitat conditions relative to documented habitat needs for specific species and life stages, including discussion of high-quality habitat, its creation, and its maintenance to inform future rehabilitation actions.

The goal of this document is to evaluate the hydraulic suitability of our four target valley segments under existing conditions to support select life stages of Chinook salmon and steelhead. This information can help identify geomorphic reaches where depth and velocity may be limiting to particular species and life stages which could prove useful for project prioritization.

1.1 Objective

Evaluate the composite suitability of geomorphic reaches in the upper Lemhi, lower Lemhi, lower Pahsimeroi, and upper Salmon (Decker Flat) valley segments based on modeled depth and velocity results available from Light Detection and Ranging (LiDAR) models available from those areas. Composite suitability is evaluated for both Chinook salmon and steelhead and for adult spawning and juvenile rearing at various discharge scenarios (see Table 2.1). We also provide the proportion of each geomorphic reach classified as simple, mixed, or complex for reference.

2 Methods

Composite suitability estimates were calculated as the geometric mean of depth and velocity suitability estimates.

2.1 Habitat Suitability

2.1.1 Chinook salmon

Figure 2.1 reference here

Figure 2.1: Suitability indices at varying depths and velocities for juvenile rearing and adult spawning for Chinook salmon from Maret et al. (2006).

2.1.2 Steelhead

Figure 2.2 reference here

Figure 2.2: Suitability indices at varying depths and velocities for juvenile rearing and adult spawning for steelhead from Maret et al. (2006).

2.2 Scenarios

And finally, I’ll reference Table 2.1 here…

Table 2.1: Scenarios for which we evaluated the composite suitability (depth & velocity) within geomorphic reaches including the corresponding depth and velocity rasters used for each scenario.

Scenario	Watershed	Species	Life Stage	Season	Depth Raster	Velocity Raster
1	Lemhi	Chinook	Juvenile	Summer	D_Aug_All.tif	V_Aug_All.tif
2	Lemhi	Chinook	Juvenile	Winter	d_jan_v2.tif	v_jan_v2.tif
3	Lemhi	Chinook	Spawning	Summer	D_Aug_All.tif	V_Aug_All.tif
4	Lemhi	Steelhead	Juvenile	Summer	D_Aug_All.tif	V_Aug_All.tif
5	Lemhi	Steelhead	Juvenile	Winter	d_jan_v2.tif	v_jan_v2.tif
6	Lemhi	Steelhead	Spawning	Spring	d_jan_v2.tif	v_jan_v2.tif
7	Pahsimeroi	Chinook	Juvenile	Summer	-	-
8	Pahsimeroi	Chinook	Juvenile	Winter	Pah_WLow_depth.tif	Pah_WLow_velocity.tif
9	Pahsimeroi	Chinook	Juvenile	Spring	Pah_1pt5_depth.tif	Pah_1pt5_velocity.tif
10	Pahsimeroi	Chinook	Spawning	Summer	Pah_WLow_depth.tif	Pah_WLow_velocity.tif
11	Pahsimeroi	Steelhead	Juvenile	Summer	-	-
12	Pahsimeroi	Steelhead	Juvenile	Winter	Pah_WLow_depth.tif	Pah_WLow_velocity.tif
13	Pahsimeroi	Steelhead	Juvenile	Spring	Pah_1pt5_depth.tif	Pah_1pt5_velocity.tif
14	Pahsimeroi	Steelhead	Spawning	Spring	Pah_1pt5_depth.tif	Pah_1pt5_velocity.tif
15	Upper Salmon	Chinook	Juvenile	Summer	US_Summer75_depth.tif	US_Summer75_velocity.tif
16	Upper Salmon	Chinook	Juvenile	Winter	US_Winter75_depth.tif	US_Winter75_velocity.tif
17	Upper Salmon	Chinook	Juvenile	Spring	US_1pt5year_depth.tif	US_1pt5year_velocity.tif
18	Upper Salmon	Chinook	Spawning	Summer	US_Summer75_depth.tif	US_Summer75_velocity.tif
19	Upper Salmon	Steelhead	Juvenile	Summer	US_Summer75_depth.tif	US_Summer75_velocity.tif
20	Upper Salmon	Steelhead	Juvenile	Winter	US_Winter75_depth.tif	US_Winter75_velocity.tif
21	Upper Salmon	Steelhead	Juvenile	Spring	US_1pt5year_depth.tif	US_1pt5year_velocity.tif
22	Upper Salmon	Steelhead	Spawning	Spring	US_1pt5year_depth.tif	US_1pt5year_velocity.tif

3 Results

Results text here…

3.1 Upper Lemhi

Figure 3.1 reference here

Figure 3.1: Violin plots showing the distribution of composite suitability values (geometric mean of depth and velocity suitability) across geomorphic reaches in the Upper Lemhi valley segment. Results for both Chinook salmon and steelhead and for three lifestages (adult spawning, juvenile summer rearing, juvenile winter rearing) are shown. The bottom panel shows the proportion of each geometric reach classified as simple, mixed, or complex.

Figure 3.2 reference here

Figure 3.2: Map showing the mean composite suitability by life stage and across geomorphic reaches for Chinook salmon and steelhead in the Upper Lemhi valley segment.

3.2 Lower Lemhi

Figure 3.3 reference here

Figure 3.3: Violin plots showing the distribution of composite suitability values (geometric mean of depth and velocity suitability) across geomorphic reaches in the Lpper Lemhi valley segment. Results for both Chinook salmon and steelhead and for three lifestages (adult spawning, juvenile summer rearing, juvenile winter rearing) are shown. The bottom panel shows the proportion of each geometric reach classified as simple, mixed, or complex.

Figure 3.4 reference here

Figure 3.4: Map showing the mean composite suitability by life stage and across geomorphic reaches for Chinook salmon and steelhead in the Lower Lemhi valley segment.

3.3 Pahsimeroi

Figure 3.5 reference here

Figure 3.5: Violin plots showing the distribution of composite suitability values (geometric mean of depth and velocity suitability) across geomorphic reaches in the Lower Pahsimeroi valley segment. Results for both Chinook salmon and steelhead and for three lifestages (adult spawning, juvenile summer rearing, juvenile winter rearing) are shown. The bottom panel shows the proportion of each geometric reach classified as simple, mixed, or complex.

Figure 3.6 reference here

Figure 3.6: Map showing the mean composite suitability by life stage and across geomorphic reaches for Chinook salmon and steelhead in the Lower Pahsimeroi valley segment.

3.4 Upper Salmon

Figure 3.7 reference here

Figure 3.7: Violin plots showing the distribution of composite suitability values (geometric mean of depth and velocity suitability) across geomorphic reaches in the Upper Salmon (Decker Flat) valley segment. Results for both Chinook salmon and steelhead and for four lifestages (adult spawning, juvenile spring rearing, juvenile summer rearing, juvenile winter rearing) are shown. The bottom panel shows the proportion of each geometric reach classified as simple, mixed, or complex.

Figure 3.8 reference here

Figure 3.8: Map showing the mean composite suitability by life stage and across geomorphic reaches for Chinook salmon and steelhead in the Upper Salmon (Decker Flat) valley segment.

4 Discussion

Some discussion crap here…

5 Literature Cited

Stuff we cite, but nobody ever actually read…